Comparative evaluation of four exome enrichment solutions in 2024: Agilent, Roche, Vazyme and Nanodigmbio.

Whole exome sequencing (WES) is essential for identifying genetic variants linked to diseases. This study compares available to date four exome enrichment kits: Agilent SureSelect Human All Exon v8, Roche KAPA HyperExome, Vazyme VAHTS Target Capture Core Exome Panel, and Nanodigmbio NEXome Plus Panel v1. We evaluated target design, coverage statistics, and variant calling accuracy across these four different exome capture products.

Heterogeneous Group of Genetically Determined Auditory Neuropathy Spectrum Disorders.

Auditory neuropathy spectrum disorder (ANSD) is often missed by standard hearing tests, accounting for up to 10% of hearing impairments (HI) and commonly linked to variants in 23 genes. We assessed 122 children with HI, including 102 with sensorineural hearing loss (SNHL) and 20 with ANSD. SNHL patients were genotyped for common variants using qPCR, while ANSD patients underwent whole exome sequencing, with variants analyzed across 249 genes.

Combined Predictors of Long-Term Outcomes of Kasai Surgery in Infants with Biliary Atresia.

Purpose: Biliary atresia (BA) is the leading cause of neonatal cholestasis (25-45%). The primary treatment is hepatic portoenterostomy (Kasai procedure), but only 20-40% provide long-term benefits. This study aimed to develop a predictive model for surgical efficacy by comparing preoperative and early postoperative indicators in infants with different outcomes.

WES-based screening of 7,000 newborns: A pilot study in Russia.

The effective implementation of whole-exome sequencing- and whole-genome sequencing-based diagnostics in the management of children affected with genetic diseases and the rapid decrease in the cost of next-generation sequencing (NGS) enables the expansion of this method to newborn genetic screening programs. Such NGS-based screening greatly increases the number of diseases that can be detected compared to conventional newborn screening, as the latter is aimed at early detection of a limited number of inborn diseases. Moreover, genetic testing provides new possibilities for family members of the proband, as many variants responsible for adult-onset conditions are inherited from the parents.

Expanding phenotype of MED13-associated syndrome presenting novel de novo missense variant in a patient with multiple congenital anomalies.

Background: Whole exome sequencing allows rapid identification of causative single nucleotide variants and short insertions/deletions in children with congenital anomalies and/or intellectual disability, which aids in accurate diagnosis, prognosis, appropriate therapeutic interventions, and family counselling. Recently, de novo variants in the MED13 gene were described in patients with an intellectual developmental disorder that included global developmental delay, mild congenital heart anomalies, and hearing and vision problems in some patients.

Results: Here we describe an infant who carried a de novo p.

Microbiome markers in HPV-positive and HPV-negative women of reproductive age with ASCUS and SIL determined by V4 region of 16S rRNA gene sequencing.

Introduction: Human papilloma virus (HPV) is the most common sexually transmitted infection worldwide. Cervicovaginal microbiota plays an important role in HPV infection and is associated with the development of squamous intraepithelial lesions (SIL). The natural history of cervical cancer involves reversible changes in the cervical tissue from a normal state, in which no neoplastic changes are detected in the squamous epithelium, to varying states of cellular abnormalities that ultimately lead to cervical cancer.

EBS in Children with De Novo Pathogenic Variants Disturbing .

Epidermolysis bullosa simplex (EBS) is a dermatological condition marked by skin fragility and blister formation resulting from separation within the basal layer of the epidermis, which can be attributed to various genetic etiologies. This study presents three pathogenic de novo variants in young children, with clinical manifestations appearing as early as the neonatal period. The variants contribute to the EBS phenotype through two distinct mechanisms: direct keratin abnormalities due to pathogenic variants in the gene, and indirect effects via pathogenic mutation in the gene, which interfere with the natural proteasome-mediated degradation pathway of KRT14.

Candidate Genes for IgA Nephropathy in Pediatric Patients: Exome-Wide Association Study.

IgA nephropathy (IgAN) is an autoimmune disorder which is believed to be non-monogenic. We performed an exome-wide association study of 70 children with IgAN and 637 healthy donors. The HLA allele frequencies were compared between the patients and healthy donors from the bone marrow registry of the Pirogov University.

CAMK2D De Novo Missense Variant in Patient with Syndromic Neurodevelopmental Disorder: A Case Report.

Background: Intellectual disability with developmental delay is the most common developmental disorder. However, this diagnosis is rarely associated with congenital cardiomyopathy. In the current report, we present the case of a patient suffering from dilated cardiomyopathy and developmental delay.

The Search of Association of HLA Class I and Class II Alleles with COVID-19 Mortality in the Russian Cohort.

HLA genes play a pivotal role in the immune response via presenting the pathogen peptides on the cell surface in a host organism. Here, we studied the association of HLA allele variants of class I (loci A, B, C) and class II (loci DRB1, DQB1, DPB1) genes with the outcome of COVID-19 infection. We performed high-resolution sequencing of class HLA I and class II genes based on the sample population of 157 patients who died from COVID-19 and 76 patients who survived despite severe symptoms.

De Novo Variant in the Gene as a Possible Cause of Neonatal Seizures.

Background: The reduction in next-generation sequencing (NGS) costs allows for using this method for newborn screening for monogenic diseases (MDs). In this report, we describe a clinical case of a newborn participating in the EXAMEN project (ClinicalTrials.gov Identifier: NCT05325749).

Description of the novel HLA-C allele, HLA-C*12:376, identified in a deceased COVID-19 patient.

The new allele HLA-C*12:376 showed one nonsynonymous nucleotide difference compared with the C*12:03:01:01 allele in codon 30.

Performance comparison of Agilent new SureSelect All Exon v8 probes with v7 probes for exome sequencing.

Exome sequencing is becoming a routine in health care, because it increases the chance of pinpointing the genetic cause of an individual patient's condition and thus making an accurate diagnosis. It is important for facilities providing genetic services to keep track of changes in the technology of exome capture in order to maximize throughput while reducing cost per sample. In this study, we focused on comparing the newly released exome probe set Agilent SureSelect Human All Exon v8 and the previous probe set v7.

gen. nov., sp. nov. and sp. nov., two novel anaerobic fermentative members of isolated from human faeces.

Three novel strains of Gram-stain-negative, obligately anaerobic, spore-forming straight or slightly curved rods with pointed ends occurring singly or in pairs were isolated from the faeces of healthy human children. The strains were characterized by mesophilic fermentative metabolism and production of acetate, ethanol and H as the end metabolic products. Strains ASD3451 and ASD5720 were motile, fermented lactose and raffinose, and weakly fermented maltose.

System analysis of the sequencing quality of human whole exome samples on BGI NGS platform.

Human exome sequencing is a classical method used in most medical genetic applications. The leaders in the field are the manufacturers of enrichment kits based on hybridization of cRNA or cDNA biotinylated probes specific for a genomic region of interest. Recently, the platforms manufactured by the Chinese company MGI Tech have become widespread in Europe and Asia.

The newborns Torque teno virus dynamics depending on the term, feeding type and maternal viral load.

The first weeks of life are extremely important for the development of the immunity-virome interaction that affects human health in adulthood. In this study we analyzed Torque teno virus (TTV) dynamics during the first weeks of life in the full-term/premature infants in relation with the maternal TTV load and the type of feeding. 152 infants aged 1-14 weeks (63 full-term and 89 premature) and 33 mother-child pairs were analyzed for the whole blood TTV load by qPCR with test sensitivity of 1000 viral copies/ml.

A novel allele, HLA-C*15:227, identified when typing COVID-19 patients.

HLA-C*15:227 differs from HLA-C*15:02:01:01 by a single nonsynonymous change (368A → G Tyrosine 99 to Cysteine).

HLA-A*11:382N, a novel HLA-A null allele identified by next-generation sequencing.

The new allele HLA-A*11:382N showed one nucleotide difference with HLA-A*11:01:01:01 at codon 254 (nonsense mutation).

Constant companion: clinical and developmental aspects of torque teno virus infections.

Torque teno virus (TTV) is a commensal human virus observed as a circular single-negative-strand DNA molecule in various tissues and biological samples, notably in blood serum and lymphocytes. TTV has no apparent clinical significance, although it might be very useful as a prospective tool for gene delivery or as an epidemiological marker. Human populations are ubiquitously infected with TTV; the prevalence may reach 100%.

Long-Term Effects of Kasai Portoenterostomy for Biliary Atresia Treatment in Russia.

This prospective study enrolled 144 patients after surgical treatment of biliary atresia in early infancy. We analyzed the immediate effectiveness of the surgery and the age-related structure of complications in the up to 16-year follow-up. The immediate 2-year survival rate after the surgery constituted 49.

NIPT Technique Based on the Use of Long Chimeric DNA Reads.

Non-invasive prenatal testing (NIPT) for aneuploidy on Chromosomes 21 (T21), 18 (T18) and 13 (T13) is actively used in clinical practice around the world. One of the limitations of the wider implementation of this test is the high cost of the analysis itself, as high-throughput sequencing is still relatively expensive. At the same time, there is an increasing trend in the length of reads yielded by sequencers.

The bacterial neurometabolic signature of the gut microbiota of young children with autism spectrum disorders.

The human gut microbiota is currently seen as an important factor that can promote autism spectrum disorder (ASD) development in children. This study aimed to detect differences in the taxonomic composition and content of bacterial genes encoding key enzymes involved in the metabolism of neuroactive biomarker compounds in the metagenomes of gut microbiota of children with ASD and neurotypical children. A whole metagenome sequencing approach was used to obtain metagenomic data on faecal specimens of 36 children with ASD and 21 healthy neurotypical children of 3-5 years old.